It will be a great day in the history of science if we sometime discover a damp shadow elsewhere in the universe where a fungus has sprouted. The mere fossil trace of life in its simplest form would be the crowning achievement of generations of brilliant and diligent labour. And here we are, a gaudy efflorescence of consciousness, staggeringly improbable in light of everything we know about the reality that contains us. There are physicists and philosophers who would correct me. They would say, if there are an infinite number of universes, as in theory there could be, then creatures like us would be very likely to emerge at some time in one of them. But to say this is only to state the fact of our improbability in other terms.

Then there is the odd privilege of existence as a coherent self, the ability to speak the word "I" and to mean by it a richly individual history of experience, perception and thought. For the religious, the sense of the soul may have as a final redoubt, not as argument but as experience, that haunting I who wakes us in the night wondering where time has gone, the I we waken to, sharply aware that we have been unfaithful to ourselves, that a life lived otherwise would have acknowledged a yearning more our own than any of the daylit motives whose behests we answer to so diligently. Our religious traditions give us as the name of God two deeply mysterious words, one deeply mysterious utterance: I AM. Putting to one side the question of their meaning as the name and character by which the God of Moses would be known, these are words any human being can say about herself, and does say, though always with a modifier of some kind. I am hungry, I am comfortable, I am a singer, I am a cook. The abrupt descent into particularity in every statement of this kind – Being itself made an auxiliary to some momentary accident of being – may only startle in the dark of night, when the intuition comes that there is no proportion between the great given of existence and the narrow vessel of circumstance into which it is inevitably forced. "I am Ozymandias, king of kings. Look on my works, ye mighty, and despair."

There is much speculation about the nature of the mind, its relation to the brain, even doubt that the word "mind" is meaningful. According to EO Wilson, "The brain and its satellite glands have now been probed to the point where no particular site remains that can reasonably be supposed to harbour a nonphysical mind". Perhaps this statement is to be taken as tongue in cheek. But to prove a negative, or to treat it as having been proved, is, oddly enough, an old and essential strategy of positivism. So I do feel obliged to point out that if such a site could be found in the brain, then the mind would be physical in the same sense that anything else with a locus in the brain is physical. To define the mind as nonphysical in the first place clearly prejudices his conclusion. Steven Pinker, on the soul, asks, "How does the spook interact with solid matter? How does an ethereal nothing respond to flashes, pokes and beeps and get arms and legs to move? Another problem is the overwhelming evidence that the mind is the activity of the brain. The supposedly immaterial soul, we now know, can be bisected with a knife, altered by chemicals," and so on. By identifying the soul with the mind, the mind with the brain, and noting the brain's vulnerability as a physical object, he feels he has debunked a conception of the soul that only those who find the word meaningless would ever have entertained.

This declension, from the ethereality of the mind/soul as spirit to the reality of the mind/brain as a lump of meat, is dependent, conceptually and for its effects, on precisely the antique dualism these writers who claim to speak for science believe they reject and refute. If complex life is the marvel we all say it is, quite possibly unique to this planet, then meat is, so to speak, that marvel in its incarnate form. It was dualism that pitted the spirit against the flesh, investing spirit with all that is lofty at the expense of flesh, which is by contrast understood as coarse and base. It only perpetuates dualist thinking to treat the physical as if it were in any way sufficiently described in disparaging terms. If the mind is the activity of the brain, this means only that the brain is capable of such lofty and astonishing things that their expression has been given the names mind, and soul, and spirit. Complex life may well be the wonder of the universe, and if it is, its status is not diminished by the fact that we can indeed bisect it, that we kill it routinely.

In any case, Wilson's conception of mind clearly has also taken on the properties of the soul, at least as that entity is understood by those eager to insist that there is no ghost in the machine. As Bertrand Russell pointed out decades before Gilbert Ryle coined this potent phrase, the old, confident distinction between materiality and nonmateriality is not a thing modern science can endorse. Physicists say a change in a split photon occurs simultaneously in its severed half, at any theoretical distance. As if there were no time or space, this information of change passes instantly from one to the other. Is an event that defies any understanding we have of causality a physical event? Yes. Can the seeming timelessness and spacelessness that mediate this change also be called physical? Presumably, since they have unambiguous physical consequences. Then perhaps we cannot claim to know the nature of the physical, and perhaps we ought not to be so confident in opposing it to a real or imagined nonphysical. These terms, as conventionally used, are not identical with the terms "real" and "unreal", though the belief that they are is the oldest tenet of positivism. The old notion of dualism should be put aside, now that we know a little about the uncanny properties of the finer textures of the physical. If, as some have suggested, quantum phenomena govern the brain, evidence for the fact is not likely to be found in scrutiny of lobes or glands or by means of any primitive understanding of the brain's materiality.

Let us say the mind is what the brain does. This is a definition that makes the mind, whatever else, a participant in the whole history and experience of the body. Pinker offers the same definition, but modifies it differently. He says, "The mind is what the brain does; specifically, the brain processes information, and thinking is a kind of computation" – excluding the felt experience of thinking, with all its diverse burdens and colorations. Elsewhere he says, with the certitude typical of his genre, "Family feelings are designed to help our genes replicate themselves, but we cannot see or smell genes . . . Our emotions about kin use a kind of inverse genetics to guess which of the organisms we interact with are likely to share our genes (for example, if someone appears to have the same parents as you do, treat the person as if their genetic wellbeing overlaps with yours)." And again we have the self we experience at a qualitative remove from what the brain really does. Presumably we are seduced into collaborating in the perpetuation of some part of our genetic inheritance by those moments of love and embrace. But why are these seductions necessary? Why are they lovely to us? Why would nature bother to distract us with them? Why do we stand apart from nature in such a way that the interests that really move us should be concealed from us? Might there not be fewer of these interfamilial crimes, honour killings, child abandonments, if nature had made us straightforwardly aware that urgencies more or less our own were being served in our propagating and nurturing? There is more than a hint of dualism in the notion that some better self – the term seems fair – has to be distracted by ingratiating pleasures to accommodate the practical business of biology.

This automaton language of Pinker's sounds a bit like Descartes. But Descartes theorised that the pineal gland, central and singular in the symmetries of the brain, moved one way or another to permit or obstruct the actions of the body, which he knew were governed by the brain. In his theory, the impressions of the senses, integrated in this gland, were appraised by the soul, which in Descartes is a term that seems pointedly synonymous with the mind. That is to say, his interest is in cognition and reason, not sin or salvation, and this in a physical and intellectual landscape inflamed by theological controversy in which those concepts figured prominently. Still, it is the soul that appraises what the mind integrates. In this way Descartes acknowledges the complexity of thinking, judging, and in his way incorporates the feeling of consciousness and the complexity of it more adequately than most theorists do now. He speaks of the mind, which he calls "I, that is to say, the mind by which I am what I am", in ways that assume it is nevertheless accessible to instruction and correction by an I that stands apart from it. To correct the syntax of his thinking so that the anomaly is removed would be to deprive it of its power as testimony – we do indeed continuously stand apart from ourselves, appraising. Every higher act of the mind, intellectual, aesthetic, or moral, is, paradoxically, also an exercise in self-doubt, self-scrutiny.

What Descartes actually intended by the words "soul" and "mind" seems to me an open question for Descartes himself. Clearly they are no mere ghost or illusion. No doubt there are volumes to be consulted on this subject. What their meanings are for us as inheritors of the thought of the modern period is a more manageable question. I am excluding the kind of thinking on this point that tends toward the model of the wager. According to this model, we place our faith in an understanding of the one thing needful, and, ultimately, suffer or triumph depending on the correctness of our choice. By these lights the soul exists primarily to be saved or lost. It is hardly more our intimate companion in mortal time than is the mind or brain by the reckoning of the positivists, behaviourists, neo-Darwinists and Freudians. The soul, in this understanding of it, is easily characterised by the nonreligious as a fearful and self-interested idea, as the product of acculturation or a fetish of the primitive brain rather than as a name for an aspect of deep experience. Therefore it is readily dismissed as a phantom of the mind, and the mind is all the more readily dismissed for its harbouring of such fears and delusions.

Descartes complains that "the philosophers of the schools accept as a maxim that there is nothing in the understanding which was not previously in the senses". The strictures of this style of thought are indeed very old. It strikes me that the word "senses" is in need of definition. As it is used, even by these schoolmen, it seems to signify only those means by which we take in information about our environment, including our own bodies, presumably. Pinker says, "The faculty with which we ponder the world has no ability to peer inside itself or our other faculties to see what makes them tick. That makes us the victims of an illusion: that our own psychology comes from some divine force or mysterious essence or almighty principle."

But the mind, or the brain, a part of the body just as Wilson says it is, is deeply sensitive to itself. Guilt, nostalgia, the pleasure of anticipation, even the shock of a realisation, all arise out of an event that occurs entirely in the mind or brain, and they are as potent as other sensations. Consistency would require a belief in the nonphysical character of the mind to exclude them from the general category of experience. If it is objected that all these things are ultimately dependent on images and sensations first gleaned from the world by the senses, this might be granted, on the condition that the sensory experience retained in the mind is understood to have the character the mind has given it. And it might be granted if sensory experience is understood to function as language does, both enabling thought and conforming it in large part to its own context, its own limitations. Anyone's sensory experience of the world is circumstantial and cultural, qualified by context and perspective, a fact which again suggests that the mind's awareness of itself is of a kind with its awareness of physical reality. The mind, like the body, is very much placed in the world. Those who claim to dismiss the mind/body dichotomy actually perpetuate it when they exclude the mind's self-awareness from among the data of human nature.

What grounds can there be for doubting that a sufficient biological account of the brain would yield the complex phenomenon we know and experience as the mind? It is only the pertinacity of the mind/body dichotomy that sustains the notion that a sufficient biological account of the brain would be reductionist in the negative sense. Such thinking is starkly at odds with our awareness of the utter brilliance of the physical body.

I do not myself believe that such an account of the brain will ever be made. Present research methods show the relatively greater activity of specific regions of the brain in response to certain stimuli or in the course of certain mental or physical behaviours. But in fact it hardly seems possible that in practice the region of the brain that yields speech would not be deeply integrated with the regions that govern social behaviour as well as memory and imagination, to degrees varying with circumstances. Nor does it seem possible that each of these would not under all circumstances profoundly modify the others, in keeping with learning and with inherited and other qualities specific to any particular brain. What should we call the presiding intelligence that orchestrates the decision to speak as a moment requires? What governs the inflections that make any utterance unmistakably the words of one speaker in this whole language-saturated world? To say it is the brain is insufficient, over-general, implying nothing about nuance and individuation. Much better to call it the mind.

If the brain at the level of complex and nuanced interaction with itself does indeed become mind, then the reductionist approach insisted upon by writers on the subject is not capable of yielding evidence of mind's existence, let alone an account of its functioning.

The strangeness of reality consistently exceeds the expectations of science, and the assumptions of science, however tried and rational, are very inclined to encourage false expectations. As a notable example, no one expected to find that the expansion of the universe is accelerating, and that the rate of its acceleration is accelerating. It is a tribute to the brilliance of science that we can know such things. And it is also an illustration of the fact that science does not foreclose possibility, including discoveries that overturn very fundamental assumptions, and that it is not a final statement about reality but a highly fruitful mode of inquiry into it.

The neo-Darwinists argue that the brain evolved to maximise the chance of genetic survival, to negotiate access to food and sex, presumably before the species evolved to the point where the prolonged helplessness of infants made genetic survival dependent in some degree on cooperation. Therefore, they tell us, we may not assume that any motive can depart from an essential qualitative likeness to these original motives. The "evolutionary epic" explains the brain exhaustively. But "the material" itself is an artifact of the scale at which we perceive. We know that we abide with quarks and constellations, in a reality unknowable by us in a degree we will never be able to calculate, but reality all the same, the stuff and the matrix of our supposedly quotidian existence. We know that within, throughout, the solid substantiality of our experience, indeterminacy reigns. Making use of the conceptual vocabulary of science to exclude a possibility that in a present state of knowledge – or a former one – that vocabulary would seem to exclude, has been the mission of positivist thinking since Auguste Comte declared scientific knowledge effectively complete. If doing so is a reflex of the polemical impulse to assert the authority of science, understandable when the project was relatively new, it is by now an atavism that persists as a consequence of this same polemical impulse. The ancient antagonist that has shaped positivism and parascientific thought and continues to inspire its missionary zeal is religion. For cultural and historical reasons, the religions against which it has opposed itself are Christianity and Judaism, both of which must be called anthropologies, whatever else. "What is man that thou art mindful of him?" The very question is an assertion that mindfulness is an attribute of God, as well as of man, a statement of the sense of deep meaning inhering in mindfulness.

If I were not a religious person, but wished to make an account of religion, I believe I would tend towards the Feuerbachian view that religion is a human projection of humanity's conceptions of beauty, goodness, power and other valued things, a humanising of experience by understanding it as structured around and mirroring back these values. Then it would resemble art, with which it is strongly associated. But this would dignify religion and characterise the mind as outwardly and imaginatively engaged with the world, as, in parascientific thought after Comte, it never is. Sigmund Freud, in Civilization and Its Discontents, says of religion, "The whole thing is so patently infantile, so foreign to reality, that to anyone with a friendly attitude to humanity it is painful to think that the great majority of mortals will never be able to rise above this view of life". Then, two pages on, he says, "The question of the purpose of human life has been raised countless times: it has never received a satisfactory answer and perhaps does not admit of one . . . Once again, only religion can answer the question of the purpose of life. One can hardly be wrong in concluding that the idea of life having a purpose stands and falls with the religious system." And then he says, "As we see, what decides the purpose of life is simply the programme of the pleasure principle. This principle dominates the operation of the mental apparatus from the start. There can be no doubt about its efficacy, and yet its programme is at loggerheads with the whole world, with the macrocosm as much as with the microcosm. There is no possibility at all of its being carried through; all the regulations of the universe run counter to it."

It seems a little strange that religion is infantile but the desire for pleasure, which "dominates the operation of the mental apparatus from the start", is not, or not, at least, in any pejorative sense. It seems strange as well that though "there is no possibility at all of its being carried out", the programme of the pleasure principle is not also, like religion, "foreign to reality". Pinker says, "Religion is a desperate measure that people resort to when the stakes are high and they have exhausted the usual techniques for the causation of success". Then a little farther on he lists the "imponderables" that lie behind the human tendency towards religion and also philosophy. These imponderables are consciousness in the sense of sentience or subjective experience, the self, free will, conceptual meaning, knowledge and morality. He says, "Maybe philosophical problems are hard not because they are divine or irreducible or meaningless or workaday science, but because the mind of Homo sapiens lacks the cognitive equipment to solve them. We are organisms, not angels, and our brains are organs, not pipelines to the truth."

How odd that these "imponderables" should be just the kind of thing humankind has pondered endlessly. Neo-Darwinism allows for hypertrophy, the phenomenon by which evolution overshoots its mark and produces some consequence not strictly useful to the ends of genetic replication, the human brain as case in point. How strange it would be, then, that this accident, this excess, should feel a tropism toward what Pinker himself calls "the truth". The great difference between parascientific thought on one hand and religion and traditional philosophy on the other is perhaps encapsulated in that word "solve", assuming the use of the word is not simply a casual imprecision. It does seem as though, for the purposes of these writers, science is the conquest of mystery, as it was for Auguste Comte and as it certainly was not for Isaac Newton. A difference between a Newton and a Comte, between science and parascience, is the desire in the latter case to treat scientific knowledge as complete, at least in its methods and assumptions, in order to further the primary object of closing questions about human nature and the human circumstance.

Science has arrived at a cluster of hypotheses about the first instant of creation. They attempt description, in the manner of science. In course of time, on various grounds, one description might prove to be more satisfactory than others. A consensus might be arrived at about the nature of a very fecund particle whose eruption became everything we know, and a great deal more beside. We might learn at some point whether time was created together with this universe or exists independently of it. The questions to which science in its most sophisticated forms has come would have been the imponderables of philosophy a few generations ago, of theology a few centuries ago, of religion a few millennia ago. Why this ancient instinct for the greatest questions? It is striking that Freud identifies religion with the meaning of life, and Pinker identifies it with the high-order questions humankind has posed to itself from antiquity. Then both writers for all purposes dismiss these things as insoluble, as if that were a legitimate reason to dismiss any question. We may never know why gravity is so much weaker than, in theory, it should be, or know if we are only one among any number of actual and potential universes. But every real question is fruitful, as the history of human thought so clearly demonstrates.

And "fruitful" is by no means a synonym for "soluble". What is man? One answer on offer is, An organism whose haunting questions perhaps ought not to be meaningful to the organ that generates them, lacking as it is in any means of "solving" them. Another answer might be, It is still too soon to tell. We might be the creature who brings life on this planet to an end, and we might be the creature who awakens to the privileges that inhere in our nature – selfhood, consciousness, even our biologically anomalous craving for "the truth" – and enjoys and enhances them. Mysteriously, neither possibility precludes the other. Our nature will describe itself as we respond to new circumstances in a world that changes continuously. So long as the human mind exists to impose itself on reality, as it has already done so profoundly, what it is and what we are must remain an open question.

Each of us lives intensely within herself or himself, continuously assimilating past and present experience to a narrative and vision that are unique in every case yet profoundly communicable, whence the arts. And we all live in a great reef of collective experience, past and present, that we receive and preserve and modify. William James says data should be thought of not as givens but as gifts, this by way of maintaining an appropriate humility in the face of what we think we know. The gifts we bring to the problem of making an account of the mind are overwhelmingly rich, severally and together. This is not an excuse for excluding them from consideration. History and civilisation are an authoritative record the mind has left, is leaving, and will leave, and objectivity deserving the name would take this record as a starting point. In practical terms, this would mean doing as the humanists have done since the building of the library of Alexandria, more or less. Humankind never ceases to express itself in new terms, and the data at hand are inevitably flawed and partial. But the complexity of the object, the human brain, and all associated phenomena are at the centre of the question, inextricable from it. The schools of thought I have criticised exclude the great fact of human exceptionalism, though no one would deny that it is a pure expression of the uniqueness of the human brain. A primary assumption of the evolutionary model behind neo-Darwinism is that development can be traced back through a series of subtly incremental changes. At what for our purposes is the terminus of all these changes there emerges, voila, the world as we know it. The neatness of this argument has always bothered me, but this is no refutation of it, nor am I interested in refuting it. I wish only to point out that there are certain things it should not be taken to imply. For example, it does not imply that a species carries forward an essential similarity to its ancestors. A bird is not a latter-day dinosaur. We can assume the ancestors ate and slept and mated, carrying on the universal business of animal life. Still, whatever the shared genetic history of beast and bird, a transformative change occurred over the millennia, and to find the modern sparrow implicit in the thunder lizard is quite certainly an error, if one wishes to make an ornithological study of sparrow behaviour. On the same grounds, there is no reason to assume our species resembles in any essential way the ancient primates whose genes we carry. It is a strategy of parascientific argument to strip away culture-making, as if it were a ruse and a concealment within which lurked the imagined primitive who is for them our true nature.

Here is another instance of evolution, to illustrate my point. The universe passed through its unimaginable first moment, first year, first billion years, wresting itself from whatever state of nonexistence, inflating, contorting, resolving into space and matter, bursting into light. Matter condenses, stars live out their generations. Then, very late, there is added to the universe of being a shaped stick or stone, a jug, a cuneiform tablet. They appear on a tiny, teetering, lopsided planet, and they demand wholly new vocabularies of description for reality at every scale. What but the energies of the universe could be expressed in the Great Wall of China, the St Matthew Passion? For our purposes, there is nothing else. Yet language that would have been fully adequate to describe the ages before the appearance of the first artifact would have had to be enlarged by concepts like agency and intention, words like creation, that would query the great universe itself. Might not the human brain, that most complex object known to exist in the universe, have undergone a qualitative change as well? If my metaphor only suggests the possibility that our species is more than an optimised ape, that something terrible and glorious befell us, a change gradualism could not predict – if this is merely another fable, it might at least encourage an imagination of humankind large enough to acknowledge some small fragment of the mystery we are.

This is an edited extract from Marilynne Robinson's Absence of Mind (Yale).